Computing and communications are well understood topics in engineering. However, we are very much at the beginning of the road to understanding those mechanisms in biological systems. I'll argue that progress in b...
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Computing and communications are well understood topics in engineering. However, we are very much at the beginning of the road to understanding those mechanisms in biological systems. I'll argue that progress in biology will require better understanding of biologically inspired paradigms for computing and communications. In particular, I'll discuss some initial results related to asynchronous circuits with feedback and to delay insensitive communications.
As more and more public and private genomic assemblies are available, the need for comparison of different computation methods used in the DNA fragment assembly becomes apparent. In this work, we design, implement, an...
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As more and more public and private genomic assemblies are available, the need for comparison of different computation methods used in the DNA fragment assembly becomes apparent. In this work, we design, implement, and test four heuristic algorithms for assembling DNA fragments. We also design, implement and test an exact algorithm to solve the fragment assembly problem.
The cybertory sequence file system (SFS) is a hybrid file-manager/database for storing and indexing large DNA sequences. It is accessed through custom functions from PostgreSQL to support queries combining database ta...
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The cybertory sequence file system (SFS) is a hybrid file-manager/database for storing and indexing large DNA sequences. It is accessed through custom functions from PostgreSQL to support queries combining database tables with custom DNA indexes and sequence access.
Computer simulation of long-range electrostatic forces in macromolecular simulation is quite challenging due to a large number of charges involved, varying dielectric constants, and ionic interactions in the solvent. ...
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Computer simulation of long-range electrostatic forces in macromolecular simulation is quite challenging due to a large number of charges involved, varying dielectric constants, and ionic interactions in the solvent. The paper introduces new difference schemes that can incorporate any desired analytical approximation of the electrostatic potential (e.g., its singular Coulombic or dipole terms) exactly, and with little computational overhead. Numerical experiments for explicit solvent models show 1-2 orders of magnitude higher accuracy in the computed energy and force, as compared to conventional Ewald summation methods with comparable parameters.
A phylogenetic tree represents the evolutionary history of a group of organisms. In this work, we introduce a novel interactive tool for constructing phylogenetic trees, phylogenetic tree construction package. The pac...
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A phylogenetic tree represents the evolutionary history of a group of organisms. In this work, we introduce a novel interactive tool for constructing phylogenetic trees, phylogenetic tree construction package. The package supports four well-known algorithms, unweighted pair group method using arithmetic average, neighbor joining, Fitch Margoliash, and maximum parsimony.
We consider the problem of interactive string searching, and propose two k-NN (k-nearest neighbor) search algorithms. For a given query, our techniques start reporting the initial results quickly. Later, these results...
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We consider the problem of interactive string searching, and propose two k-NN (k-nearest neighbor) search algorithms. For a given query, our techniques start reporting the initial results quickly. Later, these results are periodically refined depending on the user satisfaction. We briefly discuss the two techniques. The first technique, called LIS (Local statistics-based Interactive Search),and the second technique, called GIS (Global Statistics-based Interactive Search).
Although we have made progress in reducing mortality and morbidity rates in a number of human diseases through early detection and adjuvant therapy, the interventions inferred from conventional disease management and ...
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Although we have made progress in reducing mortality and morbidity rates in a number of human diseases through early detection and adjuvant therapy, the interventions inferred from conventional disease management and clinical care systems, such as those in cancers and neurological diseases, still lack discrimination and come at considerable emotional, physical, and financial cost. Complex diseases exhibit complex phenotypes, and proper diagnosis at the point-of-care requires that the analysis take into account the patient's history and exposure to environmental factors, as well as genotype and phenotype information.
A genetic algorithm has been applied to predict building schemas of protein secondary structure. This research uses protein secondary data generated by DSSP. Although the average Q3 of this research is not the highest...
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ISBN:
(纸本)0769520006
A genetic algorithm has been applied to predict building schemas of protein secondary structure. This research uses protein secondary data generated by DSSP. Although the average Q3 of this research is not the highest score among previous researches, some fundamental and useful building schemas of protein secondary structure have been found. The results of this study would be a valuable reference for understanding the basic building patterns of protein secondary structures.
We present a novel approach for rule discovery in the area of gene regulation. The method is based on supervised machine learning and is designed to reveal relationships between transcription factors and gene expressi...
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We present a novel approach for rule discovery in the area of gene regulation. The method is based on supervised machine learning and is designed to reveal relationships between transcription factors and gene expression. As a representation of the gene regulatory circuit we have chosen a special form of the IF-THEN rules associating predefined features, taken here as a generalized idea of transcription factor binding sites in gene regulatory regions, with the corresponding gene expression profiles.
This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of s...
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This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of sensitive habitats. We specifically developed bioinformatics tools for the study of (1) beach mouse communities and (2) marginal fish habitats. Data mining was used in these projects to intelligently query databases and to elucidate broad patterns that facilitate overall data interpretation. Visualization techniques that were developed present mined data in ways where context, perceptual cues, and spatial reasoning skills can be applied to uncover significant trends in behavioral patterns, habitat use, species diversity, and community composition.
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